GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpT in Synechococcus elongatus PCC 7942

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0960 Synpcc7942_0960 ATPase
          Length = 417

 Score =  183 bits (465), Expect = 6e-51
 Identities = 119/359 (33%), Positives = 185/359 (51%), Gaps = 35/359 (9%)

Query: 15  NPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTR 74
           +PQ+     L  + +E  DG    ++GPSGCGK+T+L +++GL  PS G +    R V R
Sbjct: 41  SPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDR 100

Query: 75  ASPQERNIAQVFQFPVIYDTMTVAENLAFPLRN---------------RKVP-------- 111
              + R+IA VFQ   +Y  ++V +NLAF LR                R +P        
Sbjct: 101 LPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPE 160

Query: 112 -EGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVI 170
            E +IK+RV  +A ML++   L+++   L+   KQ+++LGR + R +    L DEPL+ +
Sbjct: 161 QEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIAR-NPQVFLMDEPLSNL 219

Query: 171 DPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFER 230
           D  L+ + R ++  +  +L +T +YVTHDQ EA+T  D++ V+ RG   QV S   +++R
Sbjct: 220 DAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDR 279

Query: 231 PAHTFVGHFIGSPGMNFLPA------HRDGENLSVAGHRLASPVGRALPAGALQVGIRPE 284
           PA+ FV  FIGSP MN +P           EN          PV R      +++GIRPE
Sbjct: 280 PANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPE 339

Query: 285 YLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVGEH--TVKARFTPETRLPSSGDTAWL 341
           +L +        L  TV  V+ +G+   +  ++ E    V+AR  P+ +    GD  WL
Sbjct: 340 HLEVGAAASKNLLI-TVTGVEALGSDTFIAGELKESGIAVQARLAPQ-QCWQMGDRLWL 396


Lambda     K      H
   0.320    0.136    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 361
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 417
Length adjustment: 30
Effective length of query: 328
Effective length of database: 387
Effective search space:   126936
Effective search space used:   126936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory